scholarly journals WGS Analysis of Clonal and Plasmidic Epidemiology of Colistin-Resistance Mediated by mcr Genes in the Poultry Sector in Lebanon

2021 ◽  
Vol 12 ◽  
Author(s):  
Hiba Al-Mir ◽  
Marwan Osman ◽  
Antoine Drapeau ◽  
Monzer Hamze ◽  
Jean-Yves Madec ◽  
...  
Keyword(s):  
Poultry Meat ◽  
Whole Genome ◽  
Colistin Resistance ◽  
Whole Genome Analysis ◽  
High Genetic Diversity ◽  
E Coli ◽  
Main Driver ◽  
Comprehensive Picture ◽  
Wide Dissemination ◽  
Efficient Transfer

Poultry and poultry meat are important contributors to the global antimicrobial burden. Unregulated and illegal use of extended-spectrum cephalosporins (ESC) in this sector has long been identified as a major cause of massive spread of ESC-resistant Escherichia coli, and colistin usage is considered a main driver of plasmid-mediated mcr genes dissemination. In Lebanon, the first mcr-1-positive E. coli found in poultry dates back to 2015, followed by a few reports of mcr-1-positive E. coli in poultry, swine, humans, and the environment. On the contrary, a comprehensive picture of the population structure of mcr-1-positive E. coli and mcr-1-bearing plasmids carrying the mcr-1 gene using whole-genome analysis is largely lacking. This study reports the prevalence of mcr-1-positive E. coli in poultry originating from 32 farms across three Lebanese governorates and slaughtered in the same place. We report 27/32 (84.4%) mcr-1 positive farms, leading to a total of 84 non-duplicate E. coli collected, of which 62 presented the mcr-1 gene. Numerous associated resistances were identified, including to ESC through the presence of blaCTX–M or blaCMY genes. The mcr-1 gene was mostly carried by IncX4 (n = 36) and IncI2 (n = 24) plasmids, which are both known for their efficient transfer capacities. A high genetic diversity was detected, arguing for the lack of contamination during the slaughter process. ST744 and ST1011 were the most widely identified clones, which have been both regularly associated to mcr-1-carrying E. coli and to the poultry sector. The wide dissemination of colistin-resistance, coupled to resistances to ESC and numerous other molecules, should urge authorities to implement efficient guidelines for the use of antibiotics in the poultry sector in Lebanon.

scholarly journals Comparative Whole Genome Analysis of Escherichia coli O157:H7 Isolates From Feedlot Cattle to Identify Genotypes Associated With the Presence and Absence of stx Genes

2021 ◽  
Vol 12 ◽  
Author(s):  
Mo Jia ◽  
Ifigenia Geornaras ◽  
Jennifer N. Martin ◽  
Keith E. Belk ◽  
Hua Yang
Keyword(s):  
Escherichia Coli ◽  
Metabolic Pathway ◽  
Genome Analysis ◽  
Feedlot Cattle ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
Foodborne Outbreak ◽  
Whole Genome Analysis ◽  
E Coli ◽  
Red Recombination

A comparative whole genome analysis was performed on three newly sequenced Escherichia coli O157:H7 strains with different stx profiles, previously isolated from feedlot cattle [C1-010 (stx1−, stx2c+), C1-057 (stx−), and C1-067 (stx1+, stx2a+)], as well as five foodborne outbreak strains and six stx-negative strains from NCBI. Phylogenomic analysis demonstrated that the stx2c-carrying C1-010 and stx-negative C1-057 strains were grouped with the six NCBI stx-negative E. coli O157:H7 strains in Cluster 1, whereas the stx2a-carrying C1-067 and five foodborne outbreak strains were clustered together in Cluster 2. Based on different clusters, we selected the three newly sequenced strains, one stx2a-carrying strain, and the six NCBI stx-negative strains and identify their prophages at the stx insertion sites. All stx-carrying prophages contained both the three Red recombination genes (exo, bet, gam) and their repressor cI. On the other hand, the majority of the stx-negative prophages carried only the three Red recombination genes, but their repressor cI was absent. In the absence of the repressor cI, the consistent expression of the Red recombination genes in prophages might result in more frequent gene exchanges, potentially increasing the probability of the acquisition of stx genes. We further investigated each of the 10 selected E. coli O157:H7 strains for their respective unique metabolic pathway genes. Seven unique metabolic pathway genes in the two stx2a-carrying strains and one in the single stx2c-carrying and seven stx-negative strains were found to be associated with an upstream insertion sequence 629 within a conserved region among these strains. The presence of more unique metabolic pathway genes in stx2a-carrying E. coli O157:H7 strains may potentially increase their competitiveness in complex environments, such as feedlot cattle. For the stx2c-carrying and stx-negative E. coli O157:H7 strains, the fact that they were grouped into the same phylogenomic cluster and had the same unique metabolic pathway genes suggested that they may also share closely related evolutionary pathways. As a consequence, gene exchange between them is more likely to occur. Results from this study could potentially serve as a basis to help develop strategies to reduce the prevalence of pathogenic E. coli O157:H7 in livestock and downstream food production environments.

scholarly journals First Indian report on Genome-wide Comparison of Multidrug-ResistantEscherichia colifrom Blood Stream Infections

2019 ◽  
Author(s):  
Naveen Kumar Devanga Ragupathi ◽  
Balaji Veeraraghavan ◽  
Dhiviya Prabaa Muthuirulandi Sethuvel ◽  
Shalini Anandan ◽  
Karthick Vasudevan ◽  
...  
Keyword(s):  
Virulence Gene ◽  
Carbapenem Resistance ◽  
Blood Stream ◽  
Genome Comparison ◽  
Whole Genome ◽  
Gene Profile ◽  
Aminoglycoside Resistance ◽  
Whole Genome Analysis ◽  
E Coli ◽  
Genome Wide

AbstractBackgroundMultidrug-resistant (MDR)E. coliwith extended-spectrum β-lactamases (ESBLs) is becoming endemic in health care settings around the world. Baseline data on virulence and AMR of specific lineages ofE. colicirculating in developing countries like India is currently lacking.MethodsWhole-genome sequencing was performed for 60 MDRE. coliisolates. Genome-wide analysis was performed at single nucleotide polymorphism (SNP) level resolution to identify the relation between the isolates in context of time, virulence and AMR determinants possessed.ResultsGenome comparison revealed the presence of ST-131 global MDR and ST410 as emerging-MDR clades ofE. coli. AMR gene profile for cephalosporin and carbapenem resistance differed between the clades. GenotypesblaCTX-M-15andblaNDM-5were common among cephalosporinases and carbapenemases, respectively. For aminoglycoside resistance,rmtBwas positive for 31.7% of the isolates, of which 30% were co-harboring carbapenemases. Further, the FimH types and virulence gene profile positively correlated with the SNP based phylogeny, which also revealed the evolution of MDR clones among the study population with temporal accumulation of SNPs. The predominant clone was ST167 (blaNDMlineage) followed by ST405 (global clone ST131 equivalent) and ST410 (fast spreading high risk clone).ConclusionsThis is the first report on the whole genome analysis of MDRE. colilineages circulating in India. Data from this study will provide public health agencies a baseline portfolio of AMR and virulence in pathogenicE. coliin the region.

scholarly journals Association of Genetically Related Escherichia coli Strains with Ulcerative Colitis - A Preliminary Study

2011 ◽  
Vol 2 (2) ◽  
pp. 93-96
Author(s):  
Ritu Agarwal ◽  
Chaman Deep ◽  
Saurabh K Patel ◽  
Ashok K Jain ◽  
Gopal Nath
Keyword(s):  
Escherichia Coli ◽  
Ulcerative Colitis ◽  
Genetic Relatedness ◽  
Bacterial Species ◽  
Rectal Mucosa ◽  
Whole Genome ◽  
Medical Sciences ◽  
Whole Genome Analysis ◽  
E Coli ◽  
Major Cluster

Objective: To explore the genetic relatedness among the Escherichia coli isolates recovered from rectal mucosa of patients with Ulcerative Colitis(UC) as well as from non specific diarrhoea patients by using ERIC PCR (whole genome analysis). Material & Methods: A total of 44 strains of E coli, each from patients suffering from UC with exacerbation while on maintenance therapy, were isolated to see if there is any association with specific genotype of E coli with the clini-cal condition. For comparison, 20 strains of E coli were also isolated from patients suffering from non specific diarrhoea. These isolates were subjected to ERIC PCR for analysing similarity/ dissimilarity with each other based on the distribution of ERIC sequences in the whole genome of the bacterial species. Results: The dendrogram prepared on the basis of banding pattern showed that majority of UC patients (39/44, 88.6%) grouped in to one major cluster while second major cluster comprised mostly strains isolated from patients with non specific diarrhoea i.e. controls (17/18, 94.4%). Moreover, in the cluster representing UC patients, a total of 11 strains were observed to be genotypically similar followed by 8 strains by ERIC PCR. Conclusion: Our results strongly indicate that specific Escherichia coli strains may be involved/ associated with UC and its relapse. Key Words: Ulcerative colitis; Escherichia coli; ERIC; PCR DOI: http://dx.doi.org/10.3126/ajms.v2i2.4769Asian Journal of Medical Sciences 2 (2011) 93-96

scholarly journals Dominance of ST131Escherichia colicarryingblaCTX-Min patients with bloodstream infections caused by cephalosporin-resistant strains in Australia, New Zealand and Singapore: whole genome analysis of isolates from a randomised trial

2017 ◽  
Author(s):  
Patrick N. A. Harris ◽  
Nouri L. Ben Zakour ◽  
Leah W. Roberts ◽  
Alexander M. Wailan ◽  
Hosam M. Zowawi ◽  
...  
Keyword(s):  
New Zealand ◽  
Resistance Genes ◽  
Controlled Trial ◽  
Randomised Trial ◽  
Significant Proportion ◽  
Antibiotic Resistance Genes ◽  
Bloodstream Infections ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
E Coli

Synopsis/AbstractObjectivesTo characterise multi-drug resistantEscherichia coliisolated from patients in Australia, New Zealand and Singapore with bloodstream infection (BSI).MethodsWe prospectively collected third-generation cephalosporin resistant (3GC-R)E. colifrom blood cultures obtained from patients enrolled in a randomised controlled trial. Whole genome sequencing was used to characterise antibiotic resistance genes, sequence types (STs), plasmids and phylogenetic relationships. Antibiotic susceptibility was determined using disk diffusion and Etest.ResultsA total of 70E. coliwere included, of which the majority were ST131 (61.4%). BSI was most frequently from a urinary source (69.6%), community-associated (62.9%) and in older patients (median age 71 years [IQR 64-81]). The median Pitt bacteraemia score at presentation was 1 (IQR 0-2, range 0-3) and ICU admission was infrequent (3.1%). ST131 possessed significantly more acquired resistance genes than non-ST131 (p=0.003). Clade C1/C2 ST131 predominated (30.2% and 53.5% of all ST131 respectively) and these were all resistant to ciprofloxacin. All clade A ST131 were community-associated. The predominant ESBL types wereblaCTX-M(78.6% of isolates) and were strongly associated with ST131, with the majorityblaCTX-M-15. Clade C1 was associated withblaCTX-M-14andblaCTX-M-27, whereasblaCTX-M-15predominated in clade C2. Plasmid-mediated AmpC (p-AmpC) genes (mainlyblaCMY-2) were also frequent (17.1%) but were more common with non-ST131 strains (p< 0.001). The majority of plasmid replicon types were IncF.ConclusionsIn a prospective collection of 3GC-RE. colicausing BSI in the Australasian region, community-associated Clade C1/C2 ST131 predominate in association withblaCTX-MESBLs, although a significant proportion of non-ST131 strains carriedblaCMY-2.

scholarly journals Various Sequence Types of Escherichia coli Isolates Coharboring blaNDM-5 and mcr-1 Genes from a Commercial Swine Farm in China

2016 ◽  
Vol 61 (3) ◽  
Author(s):  
Ling-Han Kong ◽  
Chang-Wei Lei ◽  
Su-Zhen Ma ◽  
Wei Jiang ◽  
Bi-Hui Liu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Resistance Gene ◽  
Genome Sequencing ◽  
Carbapenem Resistance ◽  
Whole Genome ◽  
Swine Farm ◽  
Colistin Resistance ◽  
Content Type ◽  
E Coli ◽  
Sequence Types

ABSTRACT Sixteen different sequence types (STs) of Escherichia coli isolates from a commercial swine farm in China were confirmed to coharbor the carbapenem resistance gene bla NDM-5 and the colistin resistance gene mcr-1. Whole-genome sequencing revealed that bla NDM-5 and mcr-1 were located on a 46-kb IncX3 plasmid and a 32-kb IncX4 plasmid, respectively. The two plasmids can transfer together with a low fitness cost, which might explain the presence of various STs of E. coli coharboring bla NDM-5 and mcr-1.

scholarly journals Whole-Genome Analysis of Antimicrobial-Resistant and Extraintestinal Pathogenic Escherichia coli in River Water

2016 ◽  
Vol 83 (5) ◽  
Author(s):  
Ryota Gomi ◽  
Tomonari Matsuda ◽  
Yasufumi Matsumura ◽  
Masaki Yamamoto ◽  
Michio Tanaka ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
River Water ◽  
Surface Waters ◽  
Pathogenic Bacteria ◽  
Resistant Bacteria ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
E Coli ◽  
Resistance Determinants

ABSTRACT Contamination of surface waters by antimicrobial-resistant bacteria and pathogenic bacteria is a great concern. In this study, 531 Escherichia coli isolates obtained from the Yamato River in Japan were evaluated phenotypically for resistance to 25 antimicrobials. Seventy-six isolates (14.3%) were multidrug resistant (MDR), 66 (12.4%) were nonsusceptible to one or two classes of agents, and 389 (73.3%) were susceptible. We performed whole-genome sequencing of selected strains by using Illumina technology. In total, the genome sequences of 155 strains were analyzed for antibiotic resistance determinants and phylogenetic characteristics. More than 50 different resistance determinants, including acquired resistance genes and chromosomal resistance mutations, were detected. Among the sequenced MDR strains (n = 66), sequence type 155 (ST155) complex (n = 9), ST10 complex (n = 9), and ST69 complex (n = 7) were prevalent. Among extraintestinal pathogenic E. coli (ExPEC) strains (n = 58), clinically important clonal groups, namely, ST95 complex (n = 18), ST127 complex (n = 8), ST12 complex (n = 6), ST14 complex (n = 6), and ST131 complex (n = 6), were prevalent, demonstrating the clonal distribution of environmental ExPEC strains. Typing of the fimH (type 1 fimbrial adhesin) gene revealed that ST131 complex strains carried fimH22 or fimH41, and no strains belonging to the fimH30 subgroup were detected. Fine-scale phylogenetic analysis and virulence gene content analysis of strains belonging to the ST95 complex (one of the major clonal ExPEC groups causing community-onset infections) revealed no significant differences between environmental and clinical strains. The results indicate contamination of surface waters by E. coli strains belonging to clinically important clonal groups. IMPORTANCE The prevalence of antimicrobial-resistant and pathogenic E. coli strains in surface waters is a concern because surface waters are used as sources for drinking water, irrigation, and recreational purposes. In this study, MDR and ExPEC strains in river water were characterized by genomic sequencing and analysis. We detected more than 50 resistance determinants and identified clonal groups specific to MDR and ExPEC strains. This study showed contamination of surface waters by E. coli strains belonging to clinically important clonal groups. Overall, this study advances our understanding of environmental MDR and ExPEC strains.

scholarly journals Phylogenetic Grouping of Human Ocular Escherichia coli Based on Whole-Genome Sequence Analysis

2020 ◽  
Vol 8 (3) ◽  
pp. 422
Author(s):  
Konduri Ranjith ◽  
Chinthala Reddy SaiAbhilash ◽  
Gumpili Sai Prashanthi ◽  
Shalem Raj Padakandla ◽  
Savitri Sharma ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Phylogenetic Groups ◽  
Whole Genome Analysis ◽  
E Coli ◽  
Phylogenetic Affiliation ◽  
Antimicrobial Resistance Genes ◽  
Phylogenetic Grouping ◽  
High Concordance

Escherichia coli is a predominant bacterium in the intestinal tracts of animals. Phylogenetically, strains have been classified into seven phylogroups, A, B1, B2, C, D, E, and F. Pathogenic strains have been categorized into several pathotypes such as Enteropathogenic (EPEC), Enterotoxigenic (ETEC), Enteroinvasive (EIEC), Enteroaggregative (EAEC), Diffusely adherent (DAEC), Uropathogenic (UPEC), Shiga-toxin producing (STEC) or Enterohemorrhagic (EHEC) and Extra-intestinal pathogenic E. coli (ExPEC). E. coli also survives as a commensal on the ocular surface. However, under conditions of trauma and immune-compromised states, E. coli causes conjunctivitis, keratitis, endopthalmitis, dacyrocystitis, etc. The phylogenetic affiliation and the pathotype status of these ocular E. coli strains is not known. For this purpose, the whole-genome sequencing of the 10 ocular E. coli strains was accomplished. Based on whole-genome SNP variation, the ocular E. coli strains were assigned to phylogenetic groups A (two isolates), B2 (seven isolates), and C (one isolate). Furthermore, results indicated that ocular E. coli originated either from feces (enteropathogenic and enterotoxigenic), urine (uropathogenic), or from extra-intestinal sources (extra-intestinal pathogenic). A high concordance was observed between the presence of AMR (Antimicrobial Resistance) genes and antibiotic resistance in the ocular E. coli strains. Furthermore, several virulent genes (fimB to fimI, papB to papX, etc.) and prophages (Enterobacteria phage HK97, Enterobacteria phage P1, Escherichia phage D108 etc.) were unique to ocular E. coli. This is the first report on a whole-genome analysis of ocular E. coli strains.

scholarly journals Whole-Genome Sequencing of Multidrug-Resistant Escherichia coli Strains Harboring the mcr-1 Gene, Isolated from Seawater of the Algiers Coast in Algeria

2019 ◽  
Vol 8 (34) ◽  
Author(s):  
M. Berrazeg ◽  
A. Deriet ◽  
S. C. J. De Keersmaecker ◽  
B. Verhaegen ◽  
K. Vanneste ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Treatment Efficacy ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Colistin Resistance ◽  
Content Type ◽  
E Coli

Colistin resistance has emerged worldwide and is threatening the treatment efficacy of multiresistant Escherichia coli strains in humans and animals. Here, we communicate the whole-genome sequencing (WGS) of two colistin-resistant E. coli strains, M49 and M78, with genomes sizes of 4,947,168 and 5,178,716 bp, respectively, isolated from seawaters of the Algiers coast.

scholarly journals First Report of the Globally Disseminated IncX4 Plasmid Carrying themcr-1Gene in a Colistin-Resistant Escherichia coli Sequence Type 101 Isolate from a Human Infection in Brazil

2016 ◽  
Vol 60 (10) ◽  
pp. 6415-6417 ◽  
Author(s):  
Miriam R. Fernandes ◽  
John A. McCulloch ◽  
Marco A. Vianello ◽  
Quézia Moura ◽  
Paula J. Pérez-Chaparro ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Analysis ◽  
Human Infection ◽  
Sequence Type ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Diabetic Foot Infection ◽  
E Coli ◽  
Food Animal

ABSTRACTA colistin-resistantEscherichia colistrain was recovered from a patient with a diabetic foot infection in Brazil. Whole-genome analysis revealed that theE. coliisolate belonged to the widespread sequence type (ST) 101 and harbored themcr-1gene on an IncX4 plasmid that was highly similar tomcr-1-bearing IncX4 plasmids that were recently identified inEnterobacteriaceaefrom food, animal, and human samples recovered on different continents. These results suggest that self-transmissible IncX4-type plasmids may represent promiscuous plasmids contributing to the intercontinental spread of themcr-1gene.

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